Why are there black frames in my project?
I've tried to delete all things from the scene, then add new cube, camera and lamp. Even this doesn't help, hmm... curious setup.

But you can try create new scene via Link object and data.

1. Switch top tab to Info



2. Hit Plus to add new scene and choose Link Object Data



3. Go to Compositor and make sure you are working in a new scene



4. Now your image should render fine. (I switched plugs for Alpha Over node to show final render)